Retiring to an empty bunk room, Odo slouches down and loses his ability to hold a smooth shape; he appears to be decomposing at the cellular level. Garak enters the room suddenly and encounters an embarrassed Odo, who admits his sickness, including that changing shape makes it worse. He swears the Cardassian to secrecy; Kira mustn't find out.

Back on Deep Space 9, DoctorBashir has reached a dead end in trying to cure Odo's illness, pulling multiple all-nighters trying. ChiefO'Brien reminds the doctor that their best option is to notify CaptainSisko of their suspicions regarding Section 31, but Bashir refuses, fearing that alerting Section 31 will only make them harder to beat. He believes that science is the only answer to the problem.

Klingon chancellorGowron is trying to blame GeneralMartok for a recent defeat in battle with the Dominion at Avenal VII, even though he was outnumbered six to one. Gowron insists that a good warrior would have fought harder and found victory. Sisko sides with Martok, blaming Gowron for creating a poor battle strategy, noting that the operation was an enormous waste of resources, men and equipment. Gowron backs down, agreeing not to yet punish the severely-wounded Martok. The relationship between the two men is clearly strained.

While the Klingons are being easily defeated, the Female Changeling seeks to crush the Cardassian Rebellion as quickly as possible. She appears ragged and in a state of decomposition. Weyoun is confident that they will crush Damar's small force of terrorists quickly. She begins taking sides with ThotPran of the Breen, indicating that Weyoun had previously informed them that Damar would never turn traitor. She inquires of this Weyoun clone when the cloning facilities will be fixed, with the hint that when they are, this version of Weyoun may be replaced. She institutes strict new penalties on the citizens of Cardassia Prime, which are eerily similar to prior Cardassian policies toward Bajor during the Occupation, and also orders them to intensify their efforts to find Damar's wife and children. She also orders Pran to have his engineers accelerate the retrofitting of Jem'Hadar fighters with the Breen energy dampening weapon.

In the midst of her training sessions, Kira hatches a scheme to infiltrate a Cardassian repair facility in the Kelvas system; if they can successfully steal a Jem'Hadar ship equipped with the Breen energy dampening weapon, it may improve Starfleet's chances of finding a counter-measure. Garak warns Kira privately to not bring along Odo, because of his deteriorating condition; she admits knowing about his illness, and asks Garak to keep this secret from Odo, to improve his morale.

Sisko and Worf discuss Gowron's treatment of Martok, who will fully recover from his wounds, and Worf suggests that Gowron's motivations are political, since he feels threatened by the popularity of Martok. Worf notes shrewdly that it would not be the first time that a Klingon chancellor put his own interests ahead of the greater good. Worf has a plan – a risky plan – to stop Gowron from squandering his fleet in an attempt to discredit and humiliate Martok. At this point, Sisko does not care how risky it is, he gives Worf his support to use it, indirectly ordering Worf to make sure Gowron is removed as Chancellor. At the moment, the Klingon forces are the only ships that can stand against the Breen's energy dampening weapons.

Kira and Rusot scuffle

Tensions continue to escalate between Kira and Rusot. Rusot believes that Kira is only with them to kill more Cardassians. Rusot then crosses the line by physically touching her. She strikes him repeatedly, and then puts him into a disabling headlock. After the confrontation, a beaten Rusot vows to exact revenge after the war. When he exits, Garak emerges from the shadows, and warns Kira that Rusot will not wait until the end of the war, and she should not either. He suggests to Kira that she kill Rusot, before he kills her.

Worf asks a bedridden Martok to stand up to Gowron and challenge him for leadership of the Empire. Martok refuses to carry out a mutiny during a time of war, despite the Chancellor's reckless behavior. He argues that the Klingon High Council will never follow him if he did become Chancellor, as he has no noble blood but is a simple man from the Ketha lowlands. Worf reminds Martok that Kahless himself had no noble blood, and Martok is popular enough among Klingons that if he did become Chancellor the public support he would receive would be strong enough that the High Council would have no choice but to accept him as leader. Despite this argument, Martok refuses to even consider challenging Gowron and tells Worf to drop the matter entirely. Seeing that trying to persuade Martok is pointless, Worf is forced to give up.

Damar learns that his wife and son, in hiding since the rebellion began, have been found and killed by the Dominion. Weyoun and the Female Changeling both knew that Damar's family was not involved in the rebellion, but their deaths were ordered anyway. The grieving Damar wonders out loud how anyone could give an order to murder innocent people. Before she can stop herself, Kira asks him the same question (referencing the Cardassian Occupation of Bajor), deepening Damar's anguish and causing him to leave the room in disgust. Kira immediately regrets her outburst, but Garak tells her that the pain Damar feels now will help him give up his "romanticism" about the past, which in turn will help him lead a new Cardassia after the war.

Worf is drinking and talking with Ezri Dax about the problem with Gowron. Worf understands Martok's sentiment and so he will instead try to convince Gowron to stop his reckless attacks. He then asks her for her opinion. Ezri states that it is a Klingon matter, but Worf tells her that she has been deemed (as a successor to Jadzia) a member of the House of Martok. She warns him that he won't like what she says, but Worf insists. Ezri then explains that the problem with Gowron is part of a larger problem: The Klingon Empire is dying, and Ezri thinks it should be allowed to die. Unlike Jadzia and Curzon before her, Ezri does not view the Klingons in a romantic manner. She sees the Empire as a culture that prides itself on honor, but yet is willing to accept corruption at the highest level... Gowron is simply the latest example. Worf argues that Ezri is exaggerating, but Ezri counters by asking Worf who was the last Chancellor he respected, if there have been any, and how many times have the crimes of his leaders been covered up for the sake of the Empire. Ezri finishes by telling Worf she considers him the most honorable man she's ever met, but if he is willing to tolerate such dishonorable leaders, then there is no hope for the Empire. Worf doesn't like it, but knows that she is right.

Docking with the Jem'Hadar ship, Garak, Damar and Rusot pretend to hold Kira prisoner, seeking to present her to the Vorta commanding the ship. The Cardassian guards, who recognize Damar, allow them to pass, quietly pledging their support of the Rebellion. The shackles binding Kira's wrists suddenly morph into Odo, who promptly disappears beneath the ship's deck plates. The three Cardassians and their Bajoran "prisoner" march to the bridge and confront the commander, a female Vorta. Without warning, Odo appears on the bridge as the Female Changeling, surprising the Vorta as well as the Jem'Hadar. When the "Founder" asks to inspect a plasma rifle, Odo flips the weapon to Garak, who kills the Vorta and the Jem'Hadar warriors. Having thus secured the bridge of the enemy vessel, they nevertheless can not depart yet; the installation of the Breen weapon (in engineering) is incomplete.

Garak estimates they will need to wait precariously on the bridge for another 30 to 45 minutes. When they receive an incoming transmission for the Vorta Commander, Luaran, Kira disables the visual feed and successfully handles the routine call. They hunker down, hoping to not stir any suspicions.

O'Brien brings some crab rolls prepared by his wife Keiko to Bashir, who is slaving away working on a cure for Odo. O'Brien suggests that the doctor deviously report to Starfleet Medical that he has found a cure. This, O'Brien reasons, will lure someone from Section 31 to the station, a someone who may be able to point them in the right direction toward a real cure.

Gowron is conducting a meeting with several Klingon Generals, and announces that Martok is to attack Sarpedion V, headquarters for the Cardassian Twelfth Order, much to the disdain and concern of everyone present. Martok argues against this plan, telling Gowron that the planet is one of the most heavily fortified and the attack will most certainly fail. Gowron just uses the opportunity to insinuate that Martok is weak, and Martok is forced to agree to the attack. Worf is present and, reminded of his earlier conversation with Ezri, knows that enough is enough. He stands and tells Gowron that the attack should not be done. He claims that Gowron is dishonorable, and that he is wasting ships and lives and risking the safety of the Alpha Quadrant just so he can perform a petty act of vengeance. Gowron is incensed, and tells Worf that if he wasn't wearing a Starfleet uniform, he would kill him where he stood. Worf responds by removing his combadge, as what he is saying and doing is not as a Starfleet officer, but as a member of the House of Martok. He personally challenges Gowron's fitness to lead the Council, and Klingon honor provides only one answer to such a challenge: a duel. Both grab bat'leths and prepare for a fight to the death.

Martok tries to talk Worf out of it, but Worf has made his decision. The outcome of the entire Dominion War could rest on what is about to happen. The fight begins, and both combatants are clearly evenly matched. At a vital moment, Worf's bat'leth breaks in half, but he is able to recover and just as the chancellor is about to give Worf a killing blow, Worf is able to reach up and stab Gowron, using the two halves of the broken weapon as daggers. Gowron is dead, and Worf lets out the traditional death cry. The Chancellor's robe is immediately thrown around Worf by Martok, but as the Klingons start to chant Worf's name, Worf stops them. Worf explains that what he did was to help usher in a new era of honor and dignity for the Klingon Empire... but he is not the man to lead them into it. As Worf holds the Chancellor's mantle towards Martok, Martok protests that he has never sought the leadership. Worf reminds him that Kahless said that "great men do not seek power, they have power thrust upon them". With no further resistance, Worf drapes the robe around the general's shoulders, and calls for the room to "hail Martok, leader of the Empire! Leader of destiny."

Kira comforts a deteriorating Odo

As a depleted Odo tries to hang on to his shape, Kira comforts him. However, Rusot challenges Kira, pointing his weapon at her. He is prevented from firing by Garak, who points his weapon at Rusot. Still aiming at Kira, Rusot urges Damar to shoot Garak, pleading that they can take the Breen weapon for themselves, and, once the Dominion is gone, rebuild the Cardassian Union as the empire they both served and loved. "Just aim," Rusot urges, "and fire!" Damar aims and fires... and Rusot falls dead.

Off the amazed looks of Kira and Garak, Damar sadly explains that Rusot was his friend, but the Cardassia he believed in no longer exists – the arrogant, imperialist, xenophobic Cardassia, and its blind hatred of Bajorans. Kira and Garak are gratified – Damar is the right leader for a new Cardassia after all, just as they had hoped. They leave the station with the Breen weapon intact, while Kira comforts a quickly-deteriorating Odo.

"General Martok and I both advised you against attacking a world so deep inside Dominion territory. He was outnumbered six to one at Avenal."
"Six to one? A good commander finds ways to beat the odds, not hide behind them!"
"He didn't hide behind anything. He fought harder and longer than I would have in his place."

- Sisko and Gowron

"Seven Klingon ships destroyed. Five others severely damaged. General Martok himself in critical condition in the Rotarran Sickbay."

- Sisko, reading Worf's casualty report to Gowron

"This entire operation has been a waste of resources, men and equipment. The blame lies with the man who ordered the mission in the first place, not the man who tried to carry it out!"

- Sisko to Gowron

"If I don't want pity from the woman I love, why would I want it from you?"

- Odo, to Garak

"Julian, it's time to face facts. You're not gonna pull a rabbit out of your med kit."

- Miles O'Brien

"Exactly. If our cloning facilities were operational, I would eliminate this Weyoun immediately."

- Female Changeling, to Thot Pran

"Do whatever it takes, Mister Worf. Those Klingon ships out there are the only thing between us and the Breen. Gowron is risking the safety of the entire Alpha Quadrant and he has to stop."

- Sisko, to Worf

"They're dead. They weren't a part of this rebellion. The Dominion knew that. The Founder knew that. Weyoun knew that. To kill her and my son... the casual brutality of it... the waste of life. What kind of state tolerates the murder of innocent women and children? What kind of people give those orders?"
"Yeah, Damar, what kind of people give those orders?"

- Damar and Kira

"The general and I talked about it weeks ago. He likes you. And he considers you an honorable woman. A worthy successor to Jadzia. And so do I."
"It's very sweet of him."
"Sweet?"
"Not a very Klingon word is it?"
"No."
"It's very... honorable."
"Better... albeit a little obvious."

- Worf, telling Ezri Dax that she is a member of the House of Martok

"I think that the situation with Gowron is a symptom of a bigger problem. The Klingon Empire is dying, and I think it deserves to die."
"You're right. I do not like it!"

- Ezri and Worf

"I see a society that is in deep denial about itself. We're talking about a warrior culture that prides itself on maintaining centuries-old traditions of honor and integrity, but in reality it's willing to accept corruption at the highest levels."
"You are overstating your case."
"Am I? Who was the last leader of the High Council that you respected? Has there even been one? And how many times have you had to cover up the crimes of Klingon leaders because you were told it was for the good of the Empire?"

- Ezri and Worf

"Worf, you are the most honorable and decent man I have ever met and if you're willing to accept men like Gowron, then what hope is there for the Empire?"

- Ezri

"I will fight any battle. Anywhere. For the empire."

- Martok

"I decide what can and cannot be done."

- Gowron

"You rule without wisdom and without honor. The warriors that are gathered here will not say this to you, but I will. You are squandering our ships and our lives in a petty act of vengeance! You do not care what happens to the Empire! You only care about Gowron!"
"I should have known better than to trust you again. If you were a true Klingon I would kill you where you stand! Fortunately for you, that child's uniform shields you from your rightful fate."
(Removes his Starfleet com badge) "What I say now, I say as a member of the House of Martok, not a Starfleet officer. Gowron, son of M'Rel, you have dishonored yourself and the Empire, and you are not worthy of leading the Council."
"There can be only one answer to that!"

- Worf and Gowron

"You will not have this... day..."

- Gowron's last words

"Hail, Worf! Leader of the Empire!"

- Martok

"What I have done was for the Empire. A new day must dawn for our people. I am not the man to usher in that day. But there is a man here who can."
"Worf, I do not seek the leadership."
"Kahless said, 'Great men do not seek power... they have power thrust upon them.' "
(Worf hands the Chancellor's robes to Martok)
"Hail Martok, leader of the Empire! Leader of destiny."

- Worf and Martok

"You're still a Cardassian, Garak. You're not going to kill one of your own people for a Bajoran woman."
"How little you understand me."

- Rusot and Garak

"He was my friend. But his Cardassia is dead and won't be coming back."

As he had done with the wedding (moving it from "Strange Bedfellows" to "'Til Death Do Us Part"), René Echevarria made another major alteration to the overall plot in relation to "When It Rains...", which had a major knock-on effect on "Tacking Into the Wind"; "When I began working on "When It Rains...", the idea we'd plotted out was that Odo would learn that Section 31 had used him to give the disease to the Founders, but he was not going to get sick, just as Typhoid Mary never got sick. She just spread the disease. But as I got into it, I began thinking 'So what? So you find out something that's happened in the past. There's nothing to be done about it.' And I was a good fifteen, twenty pages in when I made the realization that Odo had to get sick. Ron already was working on "Tacking Into the Wind", and when I told him, he flipped his gourd. He said, 'No! You'll ruin everything!' But we hashed it out, and he agreed in order for this to be an ongoing storyline that mattered, Odo needed to get sick." (Star Trek: Deep Space Nine Companion)

Originally, at the end of this episode Bashir and O'Brien were to set off for a planet which they had come to learn played host to Section 31's headquarters. However, as David Weddle and Bradley Thompson were working on "Extreme Measures", which would focus on the search for a cure, it quickly became apparent that if too much money was used, there wouldn't be enough for the final episode. As such, they had to scale back the scope of the episode, and they re-located it from a planet to an interior environment. This meant, of course, that Moore had to rewrite the end of this episode so as to set it up properly. (Star Trek: Deep Space Nine Companion)

The title of this episode is a nautical reference, describing when a ship follows a course against a gale by continually making course corrections.

Initially, the plan for this episode was to have Worf simply convince Gowron that he was allowing his ego to guide his decisions and that he wasn't acting in the best interests of the Empire. Gowron would then simply return to Qo'noS and hand over control of the war effort to Martok. Ron Moore however felt that this was too simple and that it let the Klingon Empire off the hook too easily; "I wanted to view the Klingons in a different manner, and look at what I'd created with the same cold eye as Ezri. Yeah, these guys are corrupt, and Worf has put up with that for a long time. They talk a good game about how honorable they are, but they're not capable of living up to their ideals. That's an important thing to say, so let's say it." (Star Trek: Deep Space Nine Companion)

Ron Moore was a big fan of how this episode brought Kira Nerys full circle, returning her to the terrorist roots she had shed just before the series began. Indeed, bringing her back to these origins was something he'd been keen on doing for some time; "The backstory is that she's a terrorist who's become part of the establishment. There had never been a comfortable way to make her a terrorist again, although we'd had a few episodes where she'd go off and do things. But to bring her back to the 'blows-up-buildings-terrorist' would have been hard to justify. We finally were able to justify it here through circumstance." (Star Trek: Deep Space Nine Companion) Nana Visitor herself remarks, "It's interesting you know. I became a colonel, and Kira's definitely on the administrative side, and that was a whole arc for my character, she's got to use her mind and not her brawn so much. But the writers in their wisdom found a way to get me back to the beginning by sending me to Cardassia, to have to train these Cardassians to be terrorists, as I was, or freedom fighters as it were. And that brings up the old fighter in Kira and all the visceral responses and a lot of old memories. So the Kira you see in this final arc is kind of a revisit, in an interesting way. She's older, wiser, all of that, but she's still got it, she's still kinda scrappy." (Crew Dossier: Kira Nerys, DS9 Season 1 DVD, Special Features)

For his last day of shooting, actor Robert O'Reilly spent most of it on the ground playing the dead body of Gowron. At the end of the day, when filming wrapped, O'Reilly called out to Michael Dorn to help him up (as actors cannot get themselves up off the ground in full Klingon wardrobe). However, Dorn had already left the set, prompting O'Reilly to complain, "Boy, once they kill you off, they forget all about you." (Star Trek: Deep Space Nine Companion)

The words regarding power being thrust upon the worthy, ascribed to Kahless, are a paraphrase from the William Shakespeare play Twelfth Night (act II, scene 5), where the comic character Malvolio reads in a letter (sent to him in order to mock him): "...be not afraid of greatness; some are born great, some achieve greatness, and others have greatness thrust upon them."

The scene where Sisko and Gowron talk about Martok's attack on Avenal VII is longer in the script. The cut lines are as follows. Gowron says, "Martok's flagship won't return to the station for three days. That should give me time to finalize plans for our next operation." Sisko then tells him, "Chancellor, we can't afford to keep wasting ships in these reckless attacks." Gowron threateningly tells Sisko, "I like a brave man, captain... but not a foolish one. The soldiers of the Empire are mine to command. And if I say the attacks will continue... they continue." (Star Trek: Deep Space Nine Companion - A Series Guide and Script Library)

Ezri's talk with Worf about the Klingon Empire is reminiscent of Kirk's talk with Mirror Spock about the Terran Empire in "Mirror, Mirror"; in both, the Empires are on a suicide route due to their actions, and the outsider (Kirk and Ezri) pleads to the defining virtues of the member (Mirror Spock with his logic and Worf with his honor) in order to convince them to take radical action in order to save them (as opposed to just sitting back and accepting the Empire's actions and eventual fall), which they both eventually do.

This episode marks the final appearance of Robert O'Reilly as Chancellor Gowron, a role he began playing in the 1990 TNG episode "Reunion". With the death of Gowron, General Martok assumes the rank of Klingon Chancellor.

In TNG: "Reunion", Worf kills Duras, resulting in Gowron's accession to become the Chancellor; in this episode, Worf kills Gowron, thereby ending his reign. Worf was thus responsible for Gowron's rise to power and his downfall. Also, when Gowron was first named Chancellor in TNG: "Redemption", Worf felt that it was inappropriate for people to challenge Gowron during a time of war; in this episode, that sentiment is reiterated by Martok, but Worf feels that Gowron must be challenged even though the Dominion War was still going on.

In the episode "Apocalypse Rising", Worf and Gowron also engage in a fight to the death, which is interrupted by Odo fighting with the Martok Changeling. After the fight, Gowron says to Worf, "You should have killed me when you had the chance, you won't get another." "Tacking into the Wind" proved that he would.

Martok does not believe that the High Council would ever accept him as Chancellor, though "Apocalypse Rising" suggests they would have.

Armin Shimerman's wife, Kitty Swink, makes another DS9 guest appearance here as Luaran. She had made a previous guest appearance as Rozahn in "Sanctuary". Shimerman himself doesn't appear in this episode or the next (so Bashir and O'Brien meet always in an empty Quark's). He was shooting the final episodes of the third season of Buffy the Vampire Slayer, in which his character, Principal Snyder, had an important role.